Sunday 12/29/13

9:00a – 12:15a


  • Write to Ajaz about new plans
  • Read in _oligo.txt files and analyze probe distributions
  • STORM G1-G2
  • Start analysis of F12-G01 and F12-G11 data
  • continue work on STORMrender Manual


  • Reading Kieffer-Kwon et al Cell 2013. link
  • Really, insulators vary little across cell types? I don’t think this is true. Maybe it’s just lack of data at present.
  • The fundamental question of how enhancers know to talk to the right promoters seems largely un-addressed. Do we have other hypotheses aside from 3D spatial proximity? 3D spatial proximity guided by compartment formation
  • with all the talk about ‘looping out’ one would expect these HiC maps to have more check-board and less block-like structure…

Library 3 design

  • 78,225 probes using non-stringent t80 x78 s78 parameters. Room for more genome regions.
  • still need to add some black regions by parts
  • some preliminary stats:


Probe making

  • RT reactions, samples 1-8, 400 pmol primer with 10 uL of RNA solution. ~50% incorporation.
  • D12, F11, F12, G1, G2, G3, G5, G6, P1 and P3
  • F03, F04, F05, F06, G04


STORM analysis

  • running dot fitting for F12-F11 data.
  • serious issues with buffer / dye brightness. I also swear these looked better during acquisition on storm2.


  • updated STORMfinder to add an Options menu for controlling analysis parameters


  • updating professional webpage
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